feat: user doesn't skip reporting, and doesn't provide variable in params, the reporting process just doesn't happen due to empty channel

Author: atrigila

workflows/differentialabundance.nf

@@ -789,27 +789,38 @@ workflow DIFFERENTIALABUNDANCE {
         .groupTuple()                                 // [ meta, [meta with contrast], [functional results] ]
         .map { [it[0], it.tail().tail().flatten()] }  // [ meta, [functional results] ]
 
-// If users provide a `report_grouping_variable` then update the contrasts file 'variable' column with that information
+    // If users provide a `report_grouping_variable` then update the contrasts file 'variable' column with that information
+    // Split the CSV once at the start
+    ch_split = ch_validated_contrast
+        .splitCsv(header: true, sep: '\t')
+
+    // If the user provided a grouping variable, fill missing/NA values
     if (params.report_grouping_variable) {
-        ch_validated_contrast = ch_validated_contrast
-            .splitCsv(header: true, sep: '\t')
+        ch_split = ch_split
             .map { meta, row ->
                 def variable = row.variable?.trim()
                 if (!variable || variable == 'NA') {
                     row.variable = params.report_grouping_variable
                 }
                 [meta, row]
             }
-            .groupTuple()
-            .map { meta, rows ->
-                def header = rows[0].keySet().join('\t')
-                def lines = rows.collect { it.values().join('\t') }
-                def content = ([header] + lines).join('\n')
-                def outFile = file("${workflow.workDir}/${meta.id ?: meta.paramset_name}_contrast_variable_filled.tsv")
-                outFile.text = content
-                [meta, outFile]
-            }
     }
+
+    // Now remove any rows where variable is still empty
+    ch_validated_contrast = ch_split
+        .filter { meta, row ->
+            def variable = row.variable?.trim()
+            variable
+        }
+        .groupTuple()
+        .map { meta, rows ->
+            def header = rows[0].keySet().join('\t')
+            def lines = rows.collect { it.values().join('\t') }
+            def content = ([header] + lines).join('\n')
+            def outFile = file("${workflow.workDir}/${meta.id ?: meta.paramset_name}_contrast_variable_filled.tsv")
+            outFile.text = content
+            [meta, outFile]
+        }
     // Prepare input for report generation
     // Each paramset will generate one markdown report by gathering all the files created with the same paramset